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<h1>
<a href="index.html">AQUA</a></h1>

<address>
Jurgen Doreleijers, Madison, <a href="mailto:jurgenfd@gmail.com">jurgenfd@gmail.com</a></address>

<address>
Ton Rullmann, Utrecht</address>

<br>&nbsp;</td>

<td>
<blockquote>
<div align=right><img SRC="aqua.gif" height=108 width=108 align=RIGHT></div>
</blockquote>
</td>
</tr>
</table>

<h2>

<hr WIDTH="100%"></h2>

<h2>
NEW</h2>

<h2>
Contents</h2>

<ul>
<li>
<a href="#AQUA version 3.2, January 2001">LATEST VERSION (3.2, January
2001)</a></li>

<li>
<a href="#New features in version 3.0:">Version 3.0</a></li>

<li>
<a href="#New features in version 2.0:">Version 2.0</a></li>

<li>
<a href="#New features in version 1.4.1:">Version 1.4.1</a></li>

<li>
<a href="#New features in version 1.3.1:">Version 1.3.1</a></li>

<li>
<a href="#New features in version 1.2.1:">Version 1.2.1</a></li>

<li>
<a href="#New features in version 1.2.0:">Version 1.2.0</a></li>

<li>
<a href="#New features in version 1.1.0:">Version 1.1.0</a></li>

<li>
<a href="#New features in version 1.0.4:">Version 1.0.4</a></li>

<li>
<a href="#New features in version 1.0.1:">Version 1.0.1</a></li>

<li>
<a href="#AQUA version 1.0, October 8, 1996">AQUA version 1.0, October
8, 1996</a></li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="AQUA version 3.2, January 2001"></a>AQUA version 3.2, January
2001</h2>

<ul>
<li>
Clean compilation under g++ with -Wall flag</li>

<li>
Option to aqpc script allows to keep doubly occurring restraints.</li>

<li>
Option in C code and aqpc and aqdrst scripts allows for less verbose output
making it easier to read the results and find possible complications.</li>

<li>
Updated atom libraries, and routines for reading/writing PDB coordinate
file and writing NMR-STAR.</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="New features in version 3.0:"></a>New features in version 3.0:</h2>

<ul>
<li>
Module 'complchk' for analysing the completeness of NOE distance restraints.</li>

<br>This module is described in the accompanying html and text documentation
and in our paper:
<ul>
<li>
J.F. Doreleijers, M.L. Raves, J.A.C. Rullmann &amp; R. Kaptein. "Completeness
of NOEs in proteins: a statistical analysis of NMR data" J. Biomol. NMR
(1999) 14, 123-132.</li>
</ul>

<li>
Script 'aq2xplor-tors' for converting Aqua formatted torsion angle restraint
files to XPLOR format is debugged, thanks to Mia Raves.</li>

<li>
Changed the PDB nomenclature in the AtomLIB-pdb file to reflect the consensus
found for 1258 PDB entries of NMR origin. Also included such nomenclature
for nucleic acids. This means nucleic acids can now in principle (not tested)
be used for all procedures but the redundancy check.</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="New features in version 2.0:"></a>New features in version 2.0:</h2>

<ul>
<li>
Module 'assignchk' for checking and correcting consistency of stereospecific
assignments.</li>

<li>
Module 'redunchk' for checking the redundancy of NOE distance restraints.
Both modules were written by Jurgen Doreleijers, and are described in the
accompanying documentation and in our paper:</li>

<ul>
<li>
J.F. Doreleijers, J.A.C. Rullmann &amp; R. Kaptein. "Quality assessment
of NMR structures: a statistical survey" J. Mol. Biol 1998; 281(1):149-164.</li>
</ul>

<li>
Interface to WHATIF (author: Gert Vriend) check of atom nomenclature, including
protons. Procedures for correcting the nomenclature of restraints AND coordinates
without losing the stereochemical relationship between them.</li>

<li>
Script 'patchXPLORpdb' for correcting some XPLOR &lt;-> PDB differences
(see directory $AQUAEXTRASDIR)</li>

<li>
Script 'aq2xplor-tors' for converting Aqua formatted torsion angle restraint
files to XPLOR format.</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="New features in version 1.4.1:"></a>New features in version 1.4.1:</h2>

<ul>
<li>
Restraints can now be handled via R**(-6) averaging or summing instead
of the classical pseudo-atom approach. See 'qhelp aqpc' for more details.</li>

<li>
A library is now provided for handling the nomenclature of PDB files created
by MOLMOL (which slightly deviates from the standard PDB nomenclature).
The 'aqpc' script should be invoked with option -molmol.</li>

<li>
The script for converting XPLOR restraint files has been improved again
by Greg Warren.</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="New features in version 1.3.1:"></a>New features in version 1.3.1:</h2>

<ul>
<li>
The atom name mappings of methylene protons in the library for XPLOR (AtomLIB-xplor)
have been corrected. See 'qhelp xplor' for details.</li>

<li>
The 'aqpc' script now has an extra option: -ext. In this mode the external
(original) atom names are used to match restraint atoms to atoms in the
coordinate list (default: use internal names). This will work best with
"in-house" files originating from the same software environment, and can
be useful to check whether assumptions made in the Aqua libraries about
stereospecific nomenclature are indeed correct for the files currently
under investigation. (We are working on procedures for absolute checks
of stereochemistry).</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="New features in version 1.2.1:"></a>New features in version 1.2.1:</h2>

<ul>
<li>
Corrected NMR-STAR output conform latest version of dictionary. Also corrected
an error which caused the number of restraints to be be printed as 0 in
some cases (in particular for XPLOR files).</li>

<li>
Rewrote some code dealing with atom name and pseudo atom libraries. For
atom name mapping the first possible map encountered in the AtomLIB file
is now used (as in version 1.1 and earlier; in version 1.2.0 a random choice
was made when more then one mapping was possible; this only affected conversion
TO Biosym restraints). Pseudo atom lists are now ordered according to the
residue sequence.</li>

<li>
The makefile is changed and does no longer require . to be in the execution
path (which could be a nuisance if you were installing as root; thanks
to Kevin Gardner for the tip.)</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="New features in version 1.2.0:"></a>New features in version 1.2.0:</h2>

<ul>
<li>
Optional sorting of restraints and of violation lists (see 'qhelp sort').</li>

<li>
Violation lists and restraint counts per range-type (sequential, medium,
long etc.) are now included in the 'aqpc' output files.</li>

<li>
Output from restraint and violation analysis in NMR-STAR format (experimental;
see 'qhelp nmrstar').</li>

<li>
Conversion of Biosym restraints now accepts optional comments at the end
of a line.</li>

<li>
Possibility to select a residue range from a restraint file.</li>

<li>
Using model selection in 'aqpc' now selects the correct model(s).</li>

<li>
Keywords have been added to many lines in the summary output (files with
extension ending in ..sm), for easier grepping.</li>

<li>
Various improvements and bug fixes.</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="New features in version 1.1.0:"></a>New features in version 1.1.0:</h2>

<ul>
<li>
Support for restraint output (using 'aq2x') in the NMR-STAR format, for
deposition of data in the <a href="http://bmrb.wisc.edu">BioMagResBank</a>.</li>

<li>
Changes in the 'aq2x' script: modified syntax (see 'qhelp aq2x') and improvement
of efficiency (only one structure is now read from the coordinate file
to retrieve the residue list).</li>

<li>
The Aqua restraint format has been extended to accommodate distance values,
which some formats, e.g. XPLOR, define in addition to upper and lower bounds.</li>

<li>
Added "map" option to AquaWhat for remapping atom names of coordinate files.</li>

<li>
Various internal changes to menu routines.</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="New features in version 1.0.4:"></a>New features in version 1.0.4:</h2>

<ul>
<li>
Some documentation updates ('aqpc' can no longer be called from within
Procheck-NMR).</li>

<li>
Added "renum" option in AquaWhat for renumbering of residues.</li>

<li>
In PDB output:</li>

<li>
&nbsp; The largest possible atom number is 99999; when more atoms are present,
the count is now reset to 1.</li>

<li>
&nbsp; Files containing only one model are written without MODEL/ENDMDL
records.</li>

<li>
Improved exception handling in AquaPseudo/aqdrst when no pseudo atoms can
be made.</li>

<li>
The 'aqpc' and 'aq2x' scripts now replace the value of restrinp in aqua.cmm
by the value from the .noe file (cf. 'qhelp options')</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="New features in version 1.0.1:"></a>New features in version 1.0.1:</h2>

<ul>
<li>
Bug fix in convXPLORdistrestr ('qconvert' conversion of XPLOR restraint
file): corrected error which prevented restraints involving HH* to be written.</li>

<li>
Bugfix: mapping coordinate atom names when the atom name is defined as
"aqua" no longer gives an error.</li>
</ul>

<hr WIDTH="100%">
<h2>
<a NAME="AQUA version 1.0, October 8, 1996"></a>AQUA version 1.0, October
8, 1996</h2>
As a token of the new functionality of Aqua the version number has been
changed from the preliminary zero-range to a proud 1.0. This portentous
moment coincides with publication of a paper about Aqua and Procheck-NMR.
Please refer to this work in your publications of research using the Aqua
software:
<ul>
<li>
Laskowski R A, Rullmann J A C, MacArthur M W, Kaptein R &amp; Thornton
J M (1996). "AQUA and PROCHECK-NMR: Programs for checking the quality of
protein structures solved by NMR", J. Biomol. NMR 8, 477-486.</li>
</ul>
New features since version 0.40 (released April 1996):
<ul>
<li>
Code and scripts have been corrected to work on SunOS 4.1 (gcc compiler
and gawk needed) and on SunOS 5.5. See the Development Notes in README
and the installation instructions in HOW_TO_INSTALL for more details.</li>

<li>
The documentation has been considerably expanded, especially with regard
to handling of atom names, libraries etc.</li>

<li>
The installation test is functioning again.</li>

<li>
A new command: qsel. This will select residues from a PDB input file, and
write the selected range(s) to a PDB output file.</li>

<li>
A second new command: aq2x. This will convert an Aqua restraint file to
an Aqua restraint file with a different atom name format, or to a BIOSYM,
XPLOR or DIANA formatted restraint file. In combination with qconvert the
new aq2x script can be used to convert restraints between different non-Aqua
file formats.</li>

<li>
A file containing the pseudo atoms in PDB format is now created by default.
[The PROCHECK-NMR module viol2pdb uses these coordinates to visualize the
violations in a 3D structure].</li>

<li>
A new version of the convXPLORdistrestr script for converting XPLOR restraints
(provided by Greg Warren, Yale University). The script is now capable of
handling the output from the "predict" option (XPLOR 3.84): sets of assignment
alternatives, listed in OR statements, are replaced by wild cards i.e.
pseudo atoms.</li>

<li>
New libraries, using the names proposed by the IUPAC task group for the
internal nomenclature. (Warning: QR is now defined in terms of protons
instead of carbon atoms. In some cases this leads to small changes in calculated
distances and violations). Also ARG+, HIS+, LYS+, ASP- and GLU- residues
have been added to the libraries. A second, modified PDB library has been
added (PDBN). It has 2/3 nomenclature for methylene proton pairs instead
of 1/2. In the BIOSYM library R and S labels are now mapped in the appropriate
way. This replaces the old scheme in which R was always mapped on 1 and
S always on 2.</li>

<li>
Name mapping is now also applied to restraints; see 'qhelp names'.</li>

<li>
An improvement in the selection of residue ranges: when the BOTH option
is active, only selected residues appear in the output files.</li>

<li>
The efficiency of atom searches has been improved, making the code faster
especially for large proteins.</li>

<li>
Compiler directives in the code for checking restraints have been replaced
by program options (multiple, skip, guess; see 'qhelp checks').</li>

<li>
A -nosum option has been added to the aqpc script; if invoked the summary
file will not be made, which can save a lot of time.</li>

<li>
The convMRTABLE script for handling MR files (cf. 'qhelp mr') has been
improved. One change involves handling of "CHAIN X:" information found
in some name tables.</li>
</ul>

<hr>
<p>Contact the <a href="mailto:jurgenfd@gmail.com">author</a> or <a href="mailto:webmaster@bmrb.wisc.edu">webmaster</a>
for help, when required.
<br>&nbsp;
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